nextflow implementation of the facets data flow.
For vcf, see the docs over at:
https://github.com/mskcc/facets/tree/master/inst/extcode
nextflow run brwnj/facets-nf -r v1.0.0 -profile docker \
--vcf common_all.vcf.gz \
--normal normal.recal.bam \
--tumor tumor.recal.bam
The workflow runs snp-pileup and generates:
- facets.cncf
- facets.pdf
- facets.rdata